Italy had nothing to show for early dominance and after trailing 10-3 at half-time, conceded two early second-half tries in the first Test hosted by this north-eastern city.
A surprise was that none of the five Samoan tries came from 117-kilogram left-wing Alesana Tuilagi, who wreaked havoc in a 10-point win over Scotland last weekend.
South Africa, who play Scotland at the same venue in the second part of a double-header, are the likely final opponents on June 22 at Loftus Versfeld in Pretoria.
Italy were up against it even before the kick-off, needing to win by 23 points and prevent Samoa claiming a four-try bonus point if they were to go second on the table.
Despite a 10-kilogram-per-forward weight advantage, the Pacific islanders were penalised at the first two scrums and conceded early territorial and possession advantages.
But recalled fly-half Luciano Orquera fluffed his first penalty chance midway through the half and it was Samoa who broke out to open the scoring through centre and skipper Paul Williams.
Fly-half Tusi Pisi burst forward after the islanders won a midfield collision and a couple of passes later Williams was over under the crossbar for a try he converted.
Argentina-born Orquera had better luck with his second penalty attempt, a closer and less angled kick that he planted beween the posts for three points the Azzurri (Blues) thoroughly deserved.
A Williams penalty restored the seven-point Samoan advantage and an unlucky bounce close to the try-line robbed Gonzala Canale of a scoring chance after fellow centre Gonzalo Garcia just failed to land a long-range penalty kick.
Italy needed early second-half points to get back into contention, but it was the Samoans who crossed the line twice within 13 minutes and sealed a fourth win in five Tests against Italy.
A cross-field Pisi kick set up Alapati Leiua to evade two tackles and score a try and the Samoa pivot was also the creator of the next one with Johnny Leota racing in unopposed and Williams converted.
The match was more evenly contested than the 25-3 scoreline suggested, but it got worse for the Six Nations cinderella side when No. 8 Taiasina Tuifu'a dotted down and Williams converted from near the touchline.
Leiua was sin binned 10 minutes from time, Italy were awarded a penalty try converted by replacement fly-half Alberto Di Bernardo, and full-back Brando Va'aulu crossed after a break by substitute Ki Anufe, who converted.
Teams:Italy:
15 Andrea Masi, 14
Giovanbattista Venditti, 13 Gonzalo Canale, 12 Gonzalo Garcia, 11
Tommaso Iannone, 10 Luciano Orquera, 9 Edoardo Gori, 8 Sergio Parisse, 7
Marco Bergamasco, 6 Alessandro Zanni, 5 Marco Bortolami, 4 Valerie
Bernabo, 3 Martin Castrogiovanni, 2 Leonardo Ghiraldini, 1 Alberto De
Marchi
Substitutes: 16 Andrea Manici, 17 Michele Rizzo, 18 Lorenzo Cittadini, 19 Antonio Pavanello, 20 Manoa Vosawai, 21 Tobias Botes, 22 Alberto di Bernardo, 23 Luke McLean
Samoa:15 James Sooialo, 14 Alapati Leiua, 13 Paul Williams (captain), 12 John Leota, 11 Alesana Tuilagi, 10 Tusiata Pisi, 9 Jeremy Sua, 8 Taiasina Tuifua, 7 Jack Lam, 6 Ofisa Treviranus, 5 Daniel Leo, 4 Teofilo Paulo, 3 Census Johnston, 2 Wayne Ole Avei, 1 Sakaria Taulafo
Substitutes: 16 Ti'i Paulo, 17 Logovii Mulipola, 18 James Johnston, 19 Kane Thompson, 20 Junior Poluleuligaga, 21 Brando Vaaulu, 22 Seilala Mapusua, 23 Piula Faasalele
Scorers:
Samoa - 39: Tries: Paul Williams, Alapati Leiua, Johnny Leota, Taiasina Tuifu'a, Brando Va'aulu; Conversions: Williams (3), Ki Anufe; Penalties: Williams (2)
Italy - 10: Try: penalty try; Conversion: Alberto Di Bernardo; Penalty: Luciano Orquera
Sin bin:
Samoa: Leiua (70 mins)
Referee: Craig Joubert (RSA)